I've said it a million times on Twitter, but I really enjoy your VN. I know you're making a big update, but I'd love to be able to do the other story lines instead of having to start the game over.
My suggestion: Make new saves frequently. Whenever you think you're going to branch off into a new route, make a new save there and go back to the other one whenever you want to see what other decision would have led to.
I'm also bumping up the skip-text speed in this new build, so hopefully playing through the intro shouldn't take as long!